First, Shadowrath is rarely used because of their expensive resources and long training time. Also, their ability too have a long research time. So, only train Shadowrath if you found that the enemy uses Magikill, Meric, Marrowkai or Medusa. Shadowrath is meant to assassinate the enemies, not to mean that they are the main attacking force, although they stack damage upon hits. So, you must protect the Shadowrath from being killed, and after being healed, get him to battlefiled again. Don't worry, their speed is fast enough to get into battle.
As known as Ninjas, Shadowrath's speed is uncomparable by any units except Bombers.
If your enemy is using Shadowrath too, use Shinobi on the Shadowrath to prevent him from killing your spellcasters.